


Evangelion: An Angel's Gambit

by SevenWays56



Category: Neon Genesis Evangelion, Rebuild of Evangelion | Evangelion: New Theatrical Edition
Genre: F/F, F/M, Lilith Gambit, Multi, Nephilim, Nephilim Asuka, Nephilim Shinji, Yui is less then noble
Language: English
Status: In-Progress
Published: 2018-11-21
Updated: 2018-11-28
Packaged: 2019-08-27 04:29:06
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 4
Words: 15,277
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/16695448
Author URL: https://archiveofourown.org/users/SevenWays56/pseuds/SevenWays56
Summary: Third Impact seems in motion. Many groups have their plans for the event. Waking up after billions of years the mother of humanity decides to make her own play at stopping the event. Can Shinji, Asuka, and Rei succeed with the task thrust on them by the ancient angel? Or is somethings just destined to happen? Only time will tell as figures manipulate the war behind the scenes.





	1. Prologue: Awakening

**Author's Note:**

> So, yeah I am making another story. I had thought about this one after rewatching the series (and the Rebuild Movies) and I figured why not make one. So after three days, this story came into being.
> 
> This story will be more of an "Ultimate Universe" of the franchise. If you don't know tropes it means I would be using things from different continuities (like the manga, Rebuild, etc.).
> 
> Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix (?), Studio Khara and Hideaki Anno. I own nothing and please support the official release.

* * *

Pain was the first conscious feeling that she felt in… ' _How long was I out?'_  The last thing she remembered was a warning system blurring. Something about an impact and then she fell unconscious. ' _Why… why can't I move?!'_  Panic filled her as she managed to open her eyes. ' _I'm still wearing my mask.'_

She saw something happening to her legs. Being cut apart by some weird machines piloted by something. Lilith tried to reach out with her A.T field. The weak field managed to just touch the beings within the machines. If she could her eyes would widen in surprise. It was something made by her. ' _By the pit!'_  This was the worse thing she could wake up to. Her own children ripping her apart for some reason. " _Why are you doing this?!"_

Her attempt to scream with her A.T. field failed on deaf ears. She was too weak and furthermore their own A.T. fields were so weak to pick up anything. All she would succeed in doing would be to scare them. A feeling of desire through her mind at this. She was stuck like this or worse. "So, how goes the extraction process?

Her attention was pulled to two other figures walking up to the pool of her blood. Reaching out with her A.T. field she managed to catch enough of their language to at least understand what they were talking about. Reaching into the older of the group she managed to see flashes of what he knew. The first was something called Second Impact, and Adam. Lilith if she could, would be wide-eyed at the fact another Seed had landed on the world. A seed that they awoke and nearly destroyed the world!

' _By the pit, don't they know the threat that they unleashed on themselves!?'_  This wasn't supposed to even happen. They each were sent out into the void of space for different targets. Each had a target that should have been light years from each other. Even on the off chance that it did happen, they had the means to ensure that both sides didn't kill each other. That was no longer an option. ' _I have to be free it's the only chance my children have!'_

Lilith tried to link with her Longinus. Whatever was happening to her she could break it with it. The progenitor to humanity felt nothing coming to her. The all-purpose tool wasn't flying to her hands. It was destroyed by the impact. Panic consumed her before she pulled herself together. Perhaps her children had figured it out themselves? What she saw caused more questions. ' _They are using me to create things to fight Adam's spawn?'_

It sounded so wrong and yet if this was the only option that they had then what could be done? If they did manage to find her Seed-ship and her then it was possible that they could pull it off. The ancient being was content on this. If the greater good demanded it then so be it. At least her children would have a fighting chance against Adam's.

* * *

The next few weeks after the harvest Lilith just spent trying to extend her A.T. field. Gathering her strength she was able to see through the eyes of those working in the slowly being constructed facility. From what she had learned caused her pause. They didn't seem to locate anything from her seed-ship but her. At least from what they had seen. Though they seemed to have an understanding of some of the theoretical framework for many things that she knew about.

What she did see was them working on something. The designs for what could be described as a mockery of what she once was. A tool to fight the Angels as they called them. For a time Lilith while disgusted at what they were doing was content with the thought of the greater good. At least until she discovered the truth. The woman Yui, obvious to it, had explained what they were actually planning.

Lilith couldn't believe how badly they misunderstood everything. First, they thought the Dead Sea Scrolls, a corrupted warning made by her ships computers, was a means to a path to ascension. A means to either turn them into a hive mind or something. ' _What next are they planning to fuse me with Adam?'_

Her bitter thoughts aside Lilith was pissed at all of this. She had thought it was an accident that they had to awaken Adam. Nope, it turned out they were crazy enough to actually do it. That just brought them to how they had hoped to accomplish everything. ' _A hybrid?'_

Yui was getting to work on using her makeup and Lilith's in hope of creating a means to control Lilith. As she had planned her husband would find them active them and begin a means to set in motion both a plan to get her back and SEELE's while she got to complete her own plan. Speaking of Yui her plan was to become a god. ' _Is everyone here crazy?'_

As for their plan to control her, it was terrifying. They were going to rip out a part of her soul and stuff it into the clone. Lilith knew that such a forceful thing could render the newborn soul blank. A doll as Yui was hoping. Rage built up into Lilith at this. Her gaze soon caught sight through her A.T. field of Yui child. ' _They are planning for him and two other children to pilot their abominations.'_  An idea crossed the mind of the ancient being. A fiendish and dare she say it mischievous. ' _Let's see how they feel if I give the keys to them instead?'_

It was rather complex yet so simple in the end. Using their own plans against one another. The first thing to do was to find a person to influence. A few caught her eye but the one that she had planned was the current physician. With some taxing actions on her part, Lilith was able to gain control of her. When Yui's child came for a check-up Lilith now in control decided to do a little change in his check-up.

* * *

"Now, before you go I have something for you." The possessed physician walked over to a syringe with water and something else floating inside of it. As she held onto it Lilith let out a low pained groan.

Seriously if this was the pain with only a tiny bit then she was dreading what was to come later. Turning back Lilith in her bored body looked at the little boy. It was hard to think that he had no idea the kind of insanity he was going to be thrust into. For a moment Lilith hesitated to what she was going to do. Mentally reinforcing herself she looked at him. "Give me your arm."

Shinji looked a the syringe in her hand for a moment before handing her his arm. Taking it she injected the fluid into him. When she was done she tapped his shoulder. His body shivered for a second after this. "Thank you now how about I get you something for being a good boy?"

Lilith turned around as she looked through the treats the doctor had for him. The syringe contained a tiny bit of her angelic DNA. Pointless on its own but with the near insignificant bit of her soul she had managed to rip off and left into him that would change.

Already his soul was assimilating it into his own. The change in his A.T. field would cause the small DNA proteins to be copied and assimilated it as well. The effect would alter his DNA and physiology but in the end, he would become something of a hybrid. Nephilim was the name for it. "Here we are," She handed the young child a candy. "You know your future will be rather interesting."

* * *

Altering the genetic structure of one of the clones was a huge choir as she tried into the room storing the clones. Once she did she looked over the genetic makeup of each of them. A glare formed on her face due to how many errors and problems they each had. It was like they were made to be unstable. ' _Who am I kidding, of course, they were made unstable.'_

It was easier to control them if they were biologically unstable. She looked at each of the clones and their lists. "Rei?"

If she recalled Rei was one of two names that Yui was planning to call her child if Shinji had turned out to be a girl. Lilith looking over the genetic code hardened her gaze. These clones had enough genetic material to look like her physically. The rest was altered due to wild mutation or was from Lilith's. If anything she was more Rei mother then Yui. ' _You know I never had a child before.'_

True humanity was her children but that was in a figurative sense. Lilith got to work stabilizing the genome of the clones. She hit into a snag one it turned out that it would take a lot longer then she had liked. At best she could get only one of them to be fixed up. ' _Rei I is two genetically damaged though Rei II was able to be fixed.'_

Fixing the genes was rather difficult to do. The vast patchwork left several unstable genes. Nevermind the problem of Yui walking in on her. As luck would have it she was finished as the still-developing soulless clone was finished. "There we go all better now," She erased the records of what she did from the computers. With the way security was in this place, she had to make sure there was no trace to be found. Walking out of the room Lilith caught one last sight of the clones. ' _You're a true hybrid.'_

* * *

In hindsight, she should have looked up just how far they were to Germany from her home/prison. Still, her goal to subvert the plans for their first three children. Pushing back her pain she walked into the German branch with a single goal being repeated in her mind. She looked around as she pulled up the map.

' _Let's see I should go down here…'_ She stopped as she saw Asuka sitting on one of the benches. That made things a lot easier though she had an idea as to why.

Her mother was insane. Driven so due to her broken soul. SEELE was hoping that she would eventually kill herself so they can stuff her into the Evangelion they planned for her to pilot. "Asuka Langley Soryu?"

She looked up at her. The girl seemed to give her a questioning look before she noticed her name tag. As she spoke Lilith was grateful for her A.T. field being able to translate for her. "Are you the new doctor for mom?"

The ancient being felt rather bad about what was going on with her mother. However, She knew she couldn't fix what had happened. That could only cause more problems if she tried. "No, I am actually here to serve as the new physician," Taking out the clipboard that she had in order to play the part. "I was actually looking for you for your schedule check-up."

Asuka didn't seem all that happy with that. Lilith didn't know why and she didn't have much in the way of time to figure it out. Asus still went along with some minor fuss. Taking out the syringe she had packed she turned to her. "Now please give me your arm," Asuka extended her arm too her as Lilith injected the fluid into her. "Done so what do you say to a treat?"

Lilith placed her hand on her shoulder as she passed the sliver of the soul that she had prepared for her. Asuka felt a jolt go through her spine. She chose to ignore this. "No thanks."

* * *

Lilith groaned as she returned to her body the strain being almost too much for her. She took the time to let herself recuperate. Unaware to her as she was regaining her strength that now was the time that Yui choose to be absorbed into Eva-01. Those setting off events leading to his father abandoning him and learning all that Yui was working on. A plan formed in his mind. One which while ironically following both SEELE and his late wife's at first glance would have his own goals, not in others interests.

Lilith after regaining her strength in the last week knew that soon they were going to extract her part of her soul. They had managed to jerry-rig a device to do so. Lilith's A.T. field burned unto her flesh as she reached into herself. Unlike with the other two, this fragment she was about to break off was much larger. Lilith nearly fainted but in the end, she succeeded and ripped out a fresh blank angel soul from her own. Nearly blank as Lilith managed to edge something into it. The names of the other two and her mother.

As she felt this new fragment leave her Lilith felt herself fall back into a dream-like state. If she could she would have a smile on her face. Her actions had hopefully done what was needed to prevent this insane plan from coming into being. With her eyes closed, she entered into unconsciousness as her dreams were nothing but a mix of colors.

Nothing changed until she was vaguely aware of something. A minor touch on her A.T. field. An image formed within her dreams. It was close to her, close enough that in her half-conscious state that she could reach out to it. "Who are you?"

Lilith paused as she realized ho this was. It was the soul she had created from her own. The first child or Rei as the humans had called her. "My name is Lilith."

"What are you?" The question was one that had given Lilith pause. She didn't expect this to happen but it seemed that she was able to communicate with Rei even though her soul should be diverging from the piece of her own.

After thinking about it for a moment she responded to the question. "I am your mother."


	2. Chapter 1

**Notes for the Chapter:**

> Well, if you are here in America then I hope you had a happy thanksgiving. I figured I might as well post a new chapter for the day. Yeah, I tend to write the chapters with four thousand or more words so I apologize if it seems rather small. Also, this chapter can be considered a set up before I get into the story proper. Consider it the set up for the status quo moving forward.

Ever since her rebirth from being killed Rei had felt a presence in the back of her mind. The blue haired girl couldn't explain it at first but soon she had found out why. That presence was the A.T. field of Lilith which she could feel thanks to her close connection to her. Naturally, this was a surprise to learn.

The bigger surprise was that she should actually have Lilith's soul so being able to communicate with her shouldn't be possible. Keeping this revelation to herself Rei soon learned why from her mother. Lilith had ripped out a part of her own soul in order to give them something to put within the clones. ' _So, that means I am not what Commander Ikari wants me to be.'_

To the outside observer, it appeared that she was all by herself sitting with just her thoughts. Really though this wasn't the case as someone was listening to her. " _Your Commander kind of lied to you about a lot you know,"_ Lilith while still too weak to talk for prolong periods felt that this was extremely important. As such she powered through the pain. " _For instance, it wasn't him who created your clones but, his wife who I might add didn't actually love him anymore at the time she disappeared."_

Any normal person would laugh. Especially if they knew Gendo whole plans. Lilith had an idea of it having just touched his soul once before during this time. The man was madly in love and wanted to be with his wife again. ' _Then what is my purpose then?'_

Rei should tell the commander about this but she wasn't so sure. " _The plans of both the Commander and SEELE are based on misinformation and thanks to them Adam's spawn will be looking for me and him,"_ Lilith was certain that Adam wasn't dead despite blowing up. If he was alive then naturally his children would seek him out and a means to wipe out her own. " _I had fixed the patchwork of a body you currently inhabit making it actually healthy and eventually able to allow you to use your own abilities."_

That was true as she didn't feel any pain from supposed defects. In fact, her LCL treatments didn't seem to do anything for her despite it being done to help heal her ailments. Ailments that were thanks to her being a clone hybrid. Lilith's action had done away with it even allowing her body to start developing things her previous body lacked. " _I know what they are hoping to achieve and the disaster that it would become, their Human_ _Instrumentality Project_ _, as such I am hoping that you are the other two can stop it by breaking control to you three."_

Rei looked up as her body showed a physical reaction to what was going on. There were two others like her? ' _What do you mean?'_

" _The second and third children,"_ Rei understood what she was talking about. There were two other children who could pilot the Eva's one of which she knew was in Germany and the other being Vendor's sons. " _I managed, with a lot of effort, to turn them both into beings like you in order to make sure that there is no way for Third Impact to happen."_

Continuing to look in front of her Rei processed this. ' _What about the angels that we are supposed to be fighting?"_

" _They will still have to be defeated,"_ SEELE very much had a limited understanding of the relationship between her and Adam. They did know that the two of them were of different seeds but they didn't quite understand it. " _Both me and Adam represent different ideals that the First Ancestral Race once fought over and we weren't supposed to end up landing on the same world together."_

The progenitor of humanity believed that the only reason Adam's spawn will be coming to her is that they will mistake her for him. If they manage to actually find and merge with the real Adam then they would be in trouble. While it was likely that his seed-ship was destroyed they would still be able to improvise a means to wipe out her children in order to inherit the planet. Their version of Third Impact was nothing short of the extinction and terraforming of the world to their ends. " _The war will have to be fought and each one of them has to be killed."_

The blue haired girl gave her a nod. She had to cut the conversation short as Gendo walked in. Today they were hoping for her to do her first harmonic test with Eva-0. The angels were for a few years from now but that didn't change the fact that NERV was to be ready for them. Several minutes later Two was in her plug suit as she stood looking at the Eva that she was to pilot. Its metal coverings hid the fact it was actually made from Angel flesh. A fact, she remembered from her past clone.

Once she was inside she listened to the voice on the other side. The voice of Doctor Ritsuko Akagi the chief scientist of NERV. "Alright, we going to flood the LCL," Rei didn't react as the fluid filled the air around her. She knew better than anyone that it was breathable. "Alright, now let's get started."

As the test started Rei synchronization rate increased steadily. Inside it, however, she could felt vaguely aware of think. As soon as the sync started to pick up Rei's eyes shot out as she felt something around her. An unknown sensation started to boil up within her reacting to something that she didn't understand.

Outside looking over the computers Ritsuko started to notice the sudden anomalies. The scenes were going haywire as Eva-0 was starting to twitch and thrash around. Gendo looked at the actions in front of him before turning to Ritsuko. "What is going on?"

"I don't know nothing is responding to anything do!" Ritsuko had tried the emergency ejection but nothing was coming of it. "I'm cutting the power!"

Deep inside Eva-0 Rei opened her eyes as her suit started to tear apart. Behind her two wings shootout two pale white, opaque wings that looked almost like extensions of her own body before a the Rei let out a scream. Eva-0 stopped before turning off whatever happened that caused this ceasing as everyone moved into to remove a now unconscious Rei.

* * *

Lilith wasn't surprised when she felt Rei's awakening. What surprised her though was the fact that it had happened thanks to the harmonic test with Eva-0. The ancient being knew that it was made with Adam's flesh and forced in a soul from someone else. It was possible that the environment of combined with the synchronization it reacted with her physiology and awakened it. ' _I guess she will need training in use it especially for the war ahead.'_

This made her wonder about the second child and third child. Unlike Rei, their bodies were still developing into what they are to become. Lilith wondered if the same stimuli would trigger their own awaken or would it be something else? Stopping her train of thought she had to see if the effects of Rei's awakening had caused them any trouble.

Reaching out with her weakened A.T. field she did a sweep on the NERV headquarters. The scientists who deal with the Eva were looking into fixing any technical issues thinking something might have been off. Gendo the man Lilith was most concern about was taking this as a random event though he was going to keep his eye on it. ' _At least she didn't sprout her wings in front of them.'_

When they found Rei she was unconscious with her plug suit in shreds. Right now she was resting in the infirmary though if Lilith could tell it was more an aftershock from the sudden awakening. Her A.T. field had a low yet noticeable hum to it though it was hiding its true strength. Training her was going to be a huge hassle as she was certain that there was no place that Gendo wasn't going to monitor.

' _Perhaps we could try theoretical training,'_  Lilith retracted her A.T. field as she felt herself grow tired. She has used up a lot of her strength and needed to rest for a moment.

* * *

Asuka spat out the toothpaste in her mouth as she looked at herself in the mirror. Staring back at her was her blue eyes which at a distance would seem normal to anyone. However, close up one would see that her pupils were oval shaped like that of a cat. The other difference was within her mouth. Her top pair of canines had lengthened over the years looking more like fangs than anything else, while the rest of her teeth seemed to sharpen as well.

These changes always stared back at her whenever she looked in the mirror. At first, they weren't all that noticeable and when they started to become so the personnel just chalked it up to side effects of Eva piloting. A few of them even commented that it made her look threatening.

For Asuka, these changes were barely an afterthought. The one pain was how sharp her 'fangs' and teeth were. She had actually managed to bite through any eating utensil she was given. Even metal forks and spoons were quick to break under them. It also made brushing them an utter hassle as they would cut off parts of the bristles if she wasn't careful.

Still, there were several benefits to them that she wasn't complaining. Though her other habits were things that the local doctors kept her monitored over after her first few tests. Thinking about it always allowed her. ' _I mean so what if I was drinking the LCL fluid it was tasty and it's not like it was poison!'_

Another thing that brought confusion was her inability to properly inject cooked meat. Whenever she did she had to fight the urge to throw up as her stomach couldn't take it. Raw meat was a completely different story as she not only could eat it without any side effects but she actually preferred it. The usual health issues were surprisingly missing. She had a mental chuckle at this. ' _Guess I'm made of tougher stuff.'_

She walked out and down the halls of NERVes German branch as she caught a few of the doctors having a conversation. "I am telling you this is all strange that she started developing like this are we sure we don't have another pilot for reference?"

"I don't believe so," The other doctor crossed her arms. NERV was disorganized at the best of times. At the worse, each branch was known to fight among itself. "Even then do you actually think they would hear their findings with us?"

Asuka crossed her arms as she looked at the two of them. It annoyed her that they were still caught up about her weird changes. "You know I can hear you!" The two of them were using English to talk to each other but Asuka understood what they were saying perfectly enough. " _Verdammt_ , I get it already I act and look different!"

She didn't have time for this. It seemed like her changes are all that they talked about. So what they were the result of her piloting the Eva Unit? Asuka had made her choice long ago to continue even when they thought the effects were temporary. ' _Honestly, it's not like any of this matters I'm not going to sport an extra limb or anything.'_

The two doctors were left there as they watched her walk away. They both turned to each other as they looked at each other. Truth be told several things about her was starting to seem frightening to them. Besides the physical changes that could be seen it had appeared that she gained a degree of super strength. Finally, the last medical scan had picked up some kind of growth within her body. At first, everyone assumed cancer but that proved to be false when they tried looking for the signs.

She had  _grown_  a whole new organ. A completely new organ that seemingly served literally no purpose as far as they could tell. That didn't mean it wasn't vestigial or anything. By all accounts it could be doing  _something_ it's just they had no idea. "You know I'm actually scared she might try to bite out heads off," The female of the two paused at this. "And I mean that literally."

The other doctor turned to her with a raised eyebrow. "You are acting like she's some kind of monster."

"You don't think she is?"

"... No comment."

* * *

Shinji did not have the best of time after his mother died. His father abandoned him at a train station to be raised by his godparent. An old associate of his dad. A year later he noticed a change. His eyes had, something much to his confusion and that of the local doctors, developed Heterochromia. What else was neither of them were his old eye color. His right eye was a bright yellow while his left was a bright purple.

This didn't go unnoticed to the bullies at the school that he went too. This only got worse when his hair changed as well. No matter how he cut it the tips of it had turned into a bright grey color. They had spread a rumor that he had bleached it to look like even more of a freak.

The sound of the bell pulled him out of his thoughts as class was ending. Shinji picked up his books as everyone started to talk to each other about what they were hoping to do now that school was done. A few were talking about the possibility of heading off to play games, others to watch the latest movie, or just getting together. As Shinji walked out of the room he caught sight of the bullies who loved to bully him. He turned away hoping that they hadn't seen him. "Hey, Weird-eyes where do you think you are going?!"

Shinji stopped as he knew it was rather pointless to run. He had already tried and all that did was make it worse when they caught up to him. He turned to them as the stared at him with an intimidating look. "L-look I d-don't want a-any trouble."

A round of laughter escaped them at this. The leader of the trio placed his hand on his shoulder. "Really do does this mean that you wouldn't mind if we keep this then?"

One of the other two pulled out from their bag something that Shinji recognized. It was the bow to his mother's cello. Her cello was the only thing he had that belonged to her and he made sure to take care of it and everything that came with it. "H-how did you get th-that!?"

The shock and worry on his face were just what they had wanted to see. "We got it from your bag the other day figured it must have fallen in when you weren't looking," The one who held it in his hands pointed it at him. "I have to say this doesn't look like an actual bow how about we fix it for you?"

Shinji watched as the strong one of the group was handed the bow and before Shinji's very eyes broke it over his knee. The slippers of wood falling on the ground as Shinji looked at it his eyes fell on the now ruined piece of his mother's possession as they tossed it to the ground. "There much better don't you think Weird-eye?"

Shinji's mind looked on almost shutting down at this. For years he had put up with this. He had been bullied by them but never once had something like this happened. They had destroyed something his mother once owned. After a few seconds, he felt something snap in his mind. Before the knew it Shinji grabbed their leader and before everyone threw him into the lockers. Shock gripped them as they saw the dent the force of the impact had caused while Shinji looked over the bully leader.

No one moved as they just stared at him. The bully he threw into the lockers wasn't getting up as his body twitched in pain before them. As soon as he realized what he did Shinji froze in horror. ' _What just came over me?'_

Everyone who had seen this looked at him with fear. The remaining two bullies now cowered in fear at the act they had just witnessed him do to their friend. A few of the onlookers started to whisper to themselves. Shinji looked at his arms horrified at all of this. Finally, he couldn't take it and just ran out of the building.

* * *

Gendo sat in his office as he looked over everything. It was a year until the first of the Angels was destined to arrive. To years ago Rei had her incident with Eva-0 and since then they hadn't had another issue like the one from before. Rei was still making slow progress with her synchronization. After some thought, he had decided to let her wander off outside of the base and even was filling things for her to stay at her own place within the city. Under watch, of course, though he would allow her the privacy of her apartment.

Pulling out the reports he looked at the other things with his plan. His son Shinji was something he had put off for a while though with any luck things should turn out as he had hoped. "Did he start using contacts and hair dye?"

The image of his son's current appearance wasn't as he had pictured in his mind. Though his personality profile was, with a minor incident at his former school, as he had wanted it. ' _Whatever weird quirks he picked up aside it seems that the scenario will play out as I hope.'_

Placing it on the desk he looked at the report that the German branch gave him about their pilot. He suspected that a lot of it was hidden as was expected but it wasn't enough to know that everything was still as planned. ' _I will just have to request that they transfer over then.'_

Getting up from his desk he decided to take a walk across the headquarters. His first stop was to look at the Eva Units. More precisely he stopped to look the one housing the soul of his wife. It was fortunate that he had found all that she had been working on just after the incident. Now, thanks to SEELE he had the means to reunite with her.

Unknown to him someone was watching this. Rei looked at the commander almost feeling pity. The man had no idea how messed up Yui actually was due to her upbringing under SEELE. Lilith even dropped that by now whatever vestiges of a bond she once had with him was effectively gone on the part of her. Rei looked at the Eva-Unit herself as she thought about her relationship with the woman.

Yui was the one who had a huge hand in creating her body. Even using her DNA, and despite the alterations that came about due to Lilith's own, she had made sure she still looked like her. Rei could understand if someone thought that because of this that Yui was her mother or at least a parent. Knowing what she did, about how she had made her clones to fail and break apart, how her original intent was to be used as a cage for Lilith's soul, made her dismiss it.

If anyone was a parent to her it was the thing in the basement. The being who Gendo believed Rei housed the soul of. Gendo turned around and left without a word as Rei knew that he was probably going down below to talk with the crucified Lilith. A ritual that he did every few months.

* * *

Gendo stood looking at the crucified body of Lilith. Out of all the places in NERV, this one was ironically the most secure from eavesdropping from SEELE. Lilith was indisposed and seemly lifeless. As far as he knew he had Lilith walking around in the body of the clone that he had under his control.

"It's almost time for the Angels to come and with it, I only have to wait a year or two at most to be with Yui again," Gendo spoke to the giant in front of him almost like he was talking to someone.

The thing is while he was unknowingly doing so said someone couldn't speak back. Even then Lilith suspected that his reasons for talking to her was due to his declining mental health. Despite being an immediate threat should he ever find out about the truth Lilith couldn't help but pity him. ' _You have no idea what has become of her and if you did I would suspect it would either crush you or doom us all.'_

Gendo turned around placing his hand on his head as he rubbed his temples. "I just know my son will become such an annoyance to deal with when I call him in," Nevermind he will have to at some point get the second child to come to Tokyo-3. He couldn't have a wild card like that. "Still, hopefully, he'll be willing to help even if I have to force him too."

Unknown to him Lilith decided to take a look at what he had meant by that. If she could she would crush him with hands in a fit of motherly rage. He was going to purposely sabotage Rei training just before the day arrives in order to play on his son's feelings. ' _Oh, you heartless son of a bitch I take back any pity I ever had for you!'_

It was worse when she knew that Rei had to mentally suppress her ability to regenerate just to not arouse suspicion. His whole idea for manipulating his son was going to put her in needless pain. Gendo unaware of the killing intend coming off the rather enraged Lilith just went back to talking to himself. "I do wonder though if you are even aware of what I am telling you?" He adjusted his glasses at this. "Rei has shown no surprise or suspicious so I guess it's true that you're just a hollow shell."

' _Oh, I am aware of what you are telling me and so will be my daughter,'_ Rei was good at not showing emotion. A fact which both helped her avoid suspicion but also scared Lilith quite a bit. Despite the awakening of her nature, Rei's soul was still so blank. ' _You know it's actually a good thing that you abandoned your son I'm certain he would be a budding sociopath if he had you as a role model!'_

As much as she would enjoy ripping him apart, and she was  _really_  starting to enjoy the thoughts of what she could do to him, he was needed. Fighting Adams spawn would be too much of a problem without the Evas and if they did find Adam then everything will die. Curse, SEELE and their need to poke at things that they shouldn't. "Well, It was nice talking to you Lilith and sorry for cutting this short but I have to get in contact with the committee."

He turned away to leave Lilith to the fate that he thought she was in. The ancient entity didn't react at all. No, she just saved everything he said for later. Both for Rei and hopefully for the other two children when the time comes.

* * *

Shinji looked around the strange dark and almost mist covered area. Confusion was in his face as he looked for any sign of why he was here and what was going on. A sound caught his attention as he looked around frantically for the source. Out of the darkness, he saw a pair an of glowing wings giving some illumination to the mist.

Shinji turned to it as an out like of something stared as him. Two glowing eyes stared back at him. One yellow and the other purple like his own. The creature they belonged too seemed to stare back into his own eyes before he got a look at the thing as it started to rise above him. His eyes widened as he looked at the gigantic creature before him. It opened its mouth and lunged right at him.

Shinji awoke with a fright as he shot up from his bed taking in deep breaths. As he slowly calmed himself down. His mind told him that it was just a dream and yet something about it felt so real. His mind replied the events over and over again as he felt a familiarity to the creature. "Was that me?"

It was the first question to enter his mind. For a second he dismissed it as utter nonsense yet, when he did he felt like he was lying to himself. ' _No, none of this means anything it's just a dream.'_

**Notes for the Chapter:**

> As we begin our story we'll have Rei already awakened and having to hide it. I also went with giving both Shinji and Asuka different mutation then just copying how hybrids usually looked in other fanfics I tend to have read. Oh, and what was Shinji dreaming about near the end? Well, it would be spoilers. Though I can confirm that each of the children have to hit a certain sync rate with their Eva's if they want to awaken their nature (though there are possibly other ways and Eva piloting is the first I revealed). Just don't expect the next to awaken next chapter or anything like that alright.
> 
> Cya all next chapter.


	3. Chapter 2

Shinji waited for his call to go through. A small part of him was hoping that maybe his dad would answer. He got his answer when the phone just fell to an automatic answer. Talking about the city being in a state of emergency. Tokyo-3 had plenty of these drills dye to being a fortress city. "You're here."

He turned to the source of the voice. As soon as he did he was met with a girl with ice blue hair and red eyes. When he blinked in surprise she was gone. ' _Wait, was someone just standing there?'_  After a few seconds, he just chalked it up to his mind playing tricks on him. As he did an image flashed in his mind of the giant with glowing wings and eyes colored like his. ' _It's just like…'_

Shinji shook his head at this. He hadn't thought about that in over a year and yet it still lingered within his mind. Doing as he had always done he pushed it to the back of his mind. He stood out on the sidewalk as he pulled out an envelope that was sent a little after his father requested him to come to Tokyo-3. It was all his father believed was needed for him according to his caretaker. Apparently, he was being picked up by someone named Misato Katsuragi. ' _What the.'_ He pulled out a picture of her. "Well, at least I know who is coming to get…"

He was caught off guard by the sudden sounds of artillery fire and the sirens. Shinji turned around and looked wide-eyed as he saw the reflection of some giant creature in one of the skyscraper building windows. As soon as he laid eyes on it an image flashed of that giant from his dream yet again. Shinji shocked his head as he pulled himself out of it.

He turned to run before a car ended up almost running into him. Jumping out of the way it came to a stop as the door to the passer side opened up. In the driver's seat was the person from the picture Misato. "Sorry, about that but you have to come with me!"

* * *

In the NERV headquarters, Gendo watched as the military went on and continued the futile attempt at firing at the Angel. He knew it was no secret that the higher-ups in the military of both the UN and the various governments had some idea about what was actually going on. Despite SEELE efforts rumors about what had actually happened during Second Impact persisted. While none of the UN forces knew actually why the Angels were attacking they still demanded to try to take it out. ' _Foolish effort.'_

One of the U.N. commanders slammed his hand on to the console like this. They had thought that Gendo was only kidding when he said they were incapable of stopping the Angel. Watching it just ignore or casually destroy anything firing at it was starting to prove him right. "Fire the N2 bomb at it right now!"

Gendo continued to watch as a small smirk formed on his face. They were clearly starting to see how outmatched they were in this. The jets scrambled and the military forces firing started to retreat as the missile carrying one of the greatest weapons on the modern world was launched. The Angel barely registered that the missile was coming at it before it exploded tarring apart the surrounding area from the shockwave of the blast. For a moment a smile was on their faces at this. Then the dust and dirt cleared from the video feed as the Angel was still standing. "DAMN IT!"

The report of what they had done came in. The Angel was injured from the blast and while it had stopped to regenerate its A.T. Field it seemed had flared up again. Furthermore, much of the equipment had been destroyed by the shockwave of the blast. Gendo waited a few moments to let the cost of their defeat sink into their minds before he spoke. "Gentlemen I believe that this show has proven my point."

The U.N. commanders let out a sigh of defeat. "Very well then we'll let NERV take their chance at it."

As the three of them walked out Gendo looked on at the image feed. It had been fifteen years and now everything was beginning to go as planned. "Sir I must remind you that our pilot is in no condition to enter into battle."

Gendo turned to his old colleague and the closest thing he had to a confidante. Kozo Fuyutsuki the Sub-commander of NERV and one of the few who knew the full truth of the Angels. Of course, that did not mean that he knew everything. Gendo turned back to the screen as he looked at the Angel. "Misato should be bringing us a spare as we speak."

"A spare?" It took the sub-commander a few moments to realize who he was talking about. "Oh, you mean your son correct?"

Gendo turned to him for a second before giving him a slow nod. Everything should be as he had hoped with him. All he needed was to get Rei for the extra push. "The very same he is the third child."

* * *

When his father had called for him to come to Toyko-3 he did not expect for him to get pick and caught in a war zone. Yet, here he was and was now reading over the document of everything that NERV was and the Angel threat. ' _Second Impact was caused by one of those things?'_

Suddenly Shinji felt something. It wasn't in anyway he could describe but he could just feel like something was here with him. It was like it was watching him and yet Shinji couldn't place his finger on why he was feeling this. He was pulled out of his thoughts as his eyes caught sight of the giant robot before him. He spoke in a low tone at this. "What has my father been working on?"

"Misato I see you made it back with my son." Gendo stood walking into the room. As his eyes locked with his son. He hadn't seen him in nearly eleven years.

As for Shinji seeing his father brought up so many repressed feelings. A part of him wanted to yell at him for just abandoning him at a train station all those years ago. Another part wanted to know why he did that when he needed him. In the end, he didn't act on either feeling. "W-why did you c-call for me after all these y-years?"

Gendo looked at his son right in the eyes. "I need you to pilot Eva-1."

This only brought confusion on Shinji face. After a second of thought, he turned to the giant robot as he realized that his dad wanted him to pilot it. He knew he should have felt betrayed but somehow he just accepted that his father didn't care. "You only called me in to pilot a giant robot?"

"The Evangelion is not just a simple giant robot it's the peak of biomechanical engineering," Walking up to the group was Ritsuko who looked at Misato. "You know I almost thought you had gotten lost again."

Misato rolled her eyes at that remark. So, what if she had gotten lost a few times. NERV was almost like a maze unless you had a map in your hands. Even then Misato had gotten lost a few times. "Come on Ritz I'm not that hopeless with directions."

While the both of them talked Gendo looked at his son his emotions hidden under his facade. Already, he can tell that he was going to have to give him the incentive to pilot the Eva. ' _Can't play my hand in one go.'_ Adjusting his glasses Gendo spoke to his son with a calm tone. "Yes, I called you to pilot the Eva because you are the only one who can do so."

For a moment Shinji wanted to pretend that he could feel happiness at this. After having never seen him for more than a decade and never once giving a damn about him he knew that this wasn't born out of genuine care. Shinji held his head down as he felt anger swell within him. "Y-you bastard," Shinji tried to calm himself as memories of when he lashed out in anger replayed in his mind. "Why can't you get someone else to do it?!"

Nothing happened for a moment as Gendo looked at him. A lot of suppressed anger and issues had for a braid moment had broken through and revealed themselves to the Commander. He could see why Shinji reacted the way he did before. If Gendo could break his facade he would have smirked at this. ' _He is just the right about of unstable.'_  Gendo gave a look of disappointment at this. "Very well then Ritsuko please bring in Rei."

Ritsuko looked at him for a moment hesitant before giving a small nod. She turned around and motioned for the workers to bring her. Shinji's eyes widened in surprise as he saw her. The girl that appeared before him for a moment in his mind. ' _S-she's real,'_  For a moment he was lost in thought as an image of her with two wings appeared in his mind over her image. She looked so beautiful to him. When this image passed he realized just how injured she was. ' _T-they are going to make her pilot that thing in her condition?!'_

Gendo caught sight of his expression as he mentally smirked. Shinji had no idea that Rei life was unimportant given how many clones they had in the basement. In the end, she was nothing and could be replaced. "Rei I need you to pilot the Eva the spare is useless!"

Rei opened her eyes and looked at Shinji. She had sensed him enter the city and reached out to him. Making contact with her fellow Nephilim. In a brief moment, she felt how broken he was on the inside. Even with this, he had a kind heart and a desire to do what was right. He wasn't anything like his parents. As she looked at him she reached again with her A.T. field. She had felt it when she had the short contact. Shinji was mentally denying what he had become. Pulling back she turned to the Commander and spoke weakly. "Yes, sir."

Rei was about to pull herself out with her broken body when Shinji looking at this couldn't take it. He knew his father was trying to manipulate him but having someone in Rei's condition pilot a giant robot against that thing out there. "Stop!" Shinji looked at his father in the eyes. "I'll pilot the Eva."

' _Checkmate my son.'_  Everything went as he had planned. He turned back to Misato who was looking at him with a look of disbelief at his actions. "Misato gets my son suited up and Ritsuko have Eva-1 ready for launch."

Rei looked at Shinji as she was moved out of the area and headed back to the medical ward. She reached out to him again touching his dormant A.T. field with her own yet again. It was brief as she had only one thing she needed to tell him. " _You need to know what you are."_

Shinji looked in the direction of the retreating Rei and her medical bed. He stared for almost a full second before he was pulled out of his trance by Misato. This wasn't the time to think about what had just happened. He had a giant robot to pilot and an Angel to destroy. ' _This is going suck.'_

* * *

Lilith awoke as she felt the presence of one of Adams spawn nearby. She reached out to Rei wondering what was going on. " _Rei what is going on?"_

" _The third child is here and he is currently fighting the Angel using Eva-1,"_ Lilith wasn't surprised to hear this. Gendo had told her and, of course, she had told Rei about this.

Speaking of her daughter Lilith wondered what she thought about him. Even she was curious about how the third child had ended up. Geno never really talked about on how any of the children were doing when he talked to her. With Rei, she could just ask her but that wasn't a case with either of the other two children. " _Rei have you managed to talk to the third child in any way?"_

" _I made contact with him before the Angel attacked for a split second and again when the Commander pulled me out to get him to pilot the Eva,"_  Rei remembered the look he gave her when he watched her in pain. As soon as he was off to pilot the Eva she made contact with his mind one last time. " _I do think on some level he might know what he is but he seems to be suppressing the thought of it."_

On some level that was understandable. Honestly, given both him and the second child are originally human she suspected they would suppress it if they found out about it. Rei being as she is was far closer to her and with a soul that was directly ripped from her own would have no reason to suppress the fact. " _Should I tell him the truth about everything?"_

There was something that Lilith had to think about. On one hand, telling him everything might be a bit too much. Especially his mother which given how young and how long it's been he might just have forgotten about. What's worse telling him that Yui planned to get absorbed hoping for his father to dump him would probably not be best along with the knowledge that he was a Nephilim and he had to help start at least three different plans for Third Impact. " _Just tell him about his nature as a Nephilim and about the truth of the Angels and why they are attacking us the rest we'll have to tell him later."_

Suddenly Lilith felt a surge from somewhere as the presence of Adam's child was suddenly gone. If she could she would have sighed in relief at the death of one of their many foes. She didn't know how many would come but it was a start. ' _I'll need to keep a close eye on Gendo and hopefully see if I know just what the timetable is.'_

* * *

Shinji found himself within a mist covered haze of darkness all around. For a moment he saw a flash to when he was younger. Watching as his mother was talking to his grandfather. "The development of Eva-1 would be much easier with these notes," Yui held several papers in her hands. "Thank you."

His grandfather gave her a smile. "Your welcome and tell my grandson I said hi."

"I will," She waved him off as he left the room. After almost a full minute Yui started to laugh. This wasn't a kind laugh no the way it sounded sent chills down Shinji's spine. "The fool has no idea what I am actually planning to do."

The scene disappeared before him as Shinji awoke with a gasp. He was starting up at a white ceiling wondering how he had gotten here. ' _That's right I was piloting the Eva and fought that Angel.'_  As he thought about it his mind returned to the girl that his father was going to make pilot the Eva if he didn't. The girl he had seen when he first arrived. ' _Rei was her name.'_

Just before he had gotten into the robot he had heard a voice. The same one as her own if he recalled in his head. ' _You need to know what you are.'_

He wondered just what all that was about. Did he just make it all up in his head? A logical part of him believed it to be true but something within him told him that it wasn't. Shinji was interrupted from his thoughts by the sound of Misato's voice. "You're finally up."

Shinji turned his head to her. He caught sight of her outfit that she was now wearing. He was sure that she wasn't wearing it last time he saw her. "H-how long was I out?"

"About three days." Misato response made him shot up in surprise. He had been unconscious for three days!

"Th-three d-days?!" He couldn't believe it. Shinji wondered for a few moments on what he had gotten himself into. His father just called him up and effectively got him into a war zone with dangerous beings without any prior training. ' _Why me?'_

For a brief moment, he wondered if he could get out of this. That was quickly pushed back as he realized he had no idea what he was going to do. Furthermore, it wasn't like he could even go back to his old caretaker either. Shinji whispered under his breath at this. "He effectively drafted me into a war I wanted no part of," Seeing he was stuck he might as well learn what he was going to do. Turning to Misato he asked the question on his mind. "So, I'm I just going to stay here at the base?"

Misato shook her head at this. She gave him a wink. "Nope, you'll be staying with me."

* * *

There was only one thing that Gendo disliked about his job. Meeting with the overseers of NERV. Officially the organization was under the eye of the U.N. In truth SEELE the group who had in various incarnation influenced the world to differing degrees serve as the true overseers of NERV. Gendo looked at the pillars that they each used to communicate. "The Angel has been dealt with as you know and while a few rumors have popped up on the internet no one is putting much thought into it outside the conspiracy groups on the extremes of political thought."

"Perhaps, but in this day in age, the extremes have more of a voice than ever before." SEELE members knew from experience how hard it was to maintain control that they had because of them. The Second Impact and the wars that followed radicalized many sets of the population.

In a way, this was used by SEELE to help them set up NERV and its predecessor for just this task. After all, a few anonymous funding to several of the violate groups on the fringes along with the threat of growing dictatorships set up everything for the U.N. to take a more active approach in the military. "It doesn't matter by the time they find out the truth of the threat no one would be questioning the legitimacy of NERV."

Gendo continued to stand in the middle of the floating obelisks that SEELE used to talk. He knew who each of them were so there wasn't any reason for them to do so. "If I may the one who took out the Angel was your son correct?"

There was no change in Gendo expression but he knew who was asking him that. One of the few members on the SEELE inner council he actually feared. His father-in-law and Shinji grandfather. "That is correct."

"You know I think I might pay him a visit." Gendo tensed up for a fraction of a second at this. The other members of SEELE remained silent but he knew they were likely grinning and snickering at him.

He wasn't going to give them any more satisfaction in their attempts to drive him uneasily. Though he made a mental note to keep a close tab on any documents pertaining to his son. If his father-in-law got to him there was a chance he could end up turning him against the scenario. "If you don't mind I would like to return to the subject at hand."

"Very well Gendo," They did have a lot to talk about when it came to the report they were given. The U.N forces having been proven that they can't defeat an Angel was going to be moved into a supportive role as they had envisioned. "We will have all command for the Angel War given to you if any of the local forces have a problem with it let us know so that we may correct it."

A double-edged sword if he ever knew it to be. He'll have command of the U.N. forces but he knew where their loyalties lay. A very subtle way of them reminding him that he was to serve them and not an agenda that he had. They were right not to fully trust him. "Thank you."

Unknown to either of them or even Gendo someone was watching them. No matter how secure Gendo or SEELE believed this room was it was still part of the Geofront. Lilith watched silently as they spoke to one another.

* * *

Ritsuko looked at Rei as she walked into the medical ward. Most people at NERV were fed some story about her being the niece of the Commander's friend. A tale that many accepted though a few were known to question it. She knew the truth of the matter and in many ways, she actually felt pity for her.

Yui Ikari the Commander's late wife had made a whole tank filled with clones of her. Each one a mix of her DNA, or more accurately what was once her DNA, and that of the thing in the basement. Each one of them was basically sick due to their creation and had to remain in LCL fluid to stay healthy. ' _Too late to make any adjustments to stabilize her.'_

She would never say this out loud but Ritsuko hated how obsessed Gendo was with his late wife. Just looking at Rei who was basically designed by Yui to look like her was proof enough to her that the woman was likely utterly narcissistic. Perhaps she was even a bit cruel for having a girl like Rei be forced to suffer just by walking out of the tank.

Whatever the case she had in her hand the medication that Rei was supposed to take. A means to help slow the pain and help her with the side effects until they brought her in for her LCL baths. Medicine that unaware to either her or Gendo that Rei never took. Lilith had corrected all the genetic mistakes rendering the need for it pointless. True before she had made contact with her mother and learned everything she still acted as she needed it. A leftover mark from her first life when her body was close to breaking apart.

Still, she had to play the part just to keep suspicions off of her. If Gendo ever knew the truth he would be demanding answers. Answers that could very likely break him and either cause him to be replaced or worse. He might just side with Adams Angels and doom the world in despair. "Rei I have your medicine for you."

Rei turned to her as her eyes fell on the medicine. Ritsuko placed it on the counter next to her and turned to walk away. "Doctor Akagi is the Commander's son out of the medical ward?"

Ritsuko looked back at Rei with a raised eyebrow. She didn't expect Rei to ask about the boy. Perhaps she wanted to thank him for deciding to pilot and saving her life? ' _Weird, I had always pegged Rei for a death seeker.'_  Another thing that made her hate Yui and pity Rei. The pain that she was forced to suffer and her carelessness for her own life was worrying in itself. If this boy had made her rethink it then she was silently grateful. "Yes, he is currently living with Misato."

The blue haired girl gave her a nod. Lilith had told her that out on everyone at NERV she believed that Misato was the closest she could trust. If Shinji was going to learn how to properly use his Angel powers when he awakens then Rei had to train him. It would be easier if Misato was in on it and aware of the truth. "Thank you, Doctor Akagi."

Ritsuko turned and walked away. For a moment she thought about Rei living conditions. The building that Gendo left her in was practically run down. Hearing that Misato was given custody of Shinji made her remember the first time she saw the girls living arrangements. ' _For being your all-important key to everything you are treating her like she doesn't even matter to you!'_

She could bring it up with him though something told her it wouldn't matter. Perhaps she could talk to Misato about it. "Who knows maybe Shinji would have a positive influence on Rei."

* * *

Asuka bit walked into the room for training as she overheard several of the staff of NERV's German branch talk amongst themselves. A bit curious as to what they were talking about she moved closer to hear them. "I can't believe it Tokyo-3 was attacked and their Eva pilot took out an Angel!"

"Wait I thought you said that their pilot was injured?"

"That is true but my cousin told me that it was actually a new one the son of the Commander I believe."

No way was she hearing this. Some new pilot had managed to take out an Angel without any training. Asuka was both impressed and had a bit of a hit to her pride. Yet, something within her wanted to go and meet this pilot. She couldn't answer as to why this was though. "I want to head to Tokyo-3."

The staff all turned to her a bit surprised by her sudden demand. The personnel looked at her other for a few seconds wondering if they should. After a while one of them decided to speak up at her request. "I'll see what I can do about that."

**Notes for the Chapter:**

> So, I figured I shouldn't write the first battle due to it effectively just being as I was planning a near copy of the anime. My apologies for skipping it. Though, that shouldn't be a problem as we go on. Anyway, I might hold off the next update for a while or I might not. I do have quite a few stories after all. We will just see how my inspiration goes.


	4. Chapter 3

* * *

The call he had gotten was unexpected. Yet, He saw an opportunity and was quick to take it. After a half an hour of negotiations, it seemed he finally had the Second Child under his watchful eye. They were just going to have to make a few changes to help with accommodating her. ' _Misato has an extra room in her apartment and perhaps…'_

He was cut from his thoughts as Ritsuko walked in. The chief scientist looked at him with a bit of an enraged look on her face. "What is the meaning of this?"

Gendo knew what she was referring too. Truthfully he knew about how attached the doctor had gotten to Rei when she found out about the clones. The creations of his late wife that she made in order to contain the soul of Lilith. At first, she was rather fearful of her and she was rather justified in that thought. She was afraid of the fact they had an actual Angel on par with Adam in their mists and walking around. Although after seeing how empty and almost how broken and, in a certain way, sad she quickly became attached and worried for her well being.

As of now he could actually see her almost adopting Rei if there was an option. It was both bother a benefit and a problem. He didn't have to worry about her abusing Rei or being fearful of their relationship. The negative was that she was vocal about his treatment of her. "I did tell you to read the whole thing over when you agreed to it, Doctor Akagi."

"You know the building she is living in isn't safe so how could you leave her there?" Ritsuko wrapped back at him. Gendo had chosen it for a few reasons. Each one rather subtle though in the end, it was rather cheap and not as if anyone would question it.

A thought crossed his mind. The Second Child was rather competitive. She was coming here to likely meet with his son due to him taking out an Angel. Perhaps he could use this to further ensure things went as he hoped. "If you wish I might be able to allow something about that."

* * *

If there was one thing Shinji dreaded it was going back to public school. The last time he went there it was a slow agony. When he learned his father had arranged it Shinji just rolled his eyes at this. Of course, his dear old dad was making him do this. ' _At least things aren't as bad as they were.'_

A few of the students were actually, friendly with him. Two of them being Kensuke Aide and Toji Suzuhara who knew that he was a pilot and about the truth of what had happened when the Angel attacked. Considering the news was trying to spin it as some sort of freak monster created in the aftermath of Second Impact, and a lot of people seemed to by buying it on the internet, this was surprising. Kansuke explained that his father and grandfather both work for NERV so he was able to discover it from their reports.

By the end of the day, Shinji was actually a bit hopeful. People did comment on his dual colored hair and eyes but no one really made a fuss about it. although a few did point out that he was kind of like the other new student they had gotten a year ago. Shinji looked at the empty desk next to him. It was where Rei would sit in the class. "Shinji," Shinji looked up to his homeroom teacher as class was just about to end. "I need you to give Rei her homework for the day."

Shinji looked at the teacher who handed him Rei's homework. According to Misato, the school was informed about him being part of the same program at NERV but nothing much beyond that. It seemed the same was true for Rei. So, it would make sense for him to be chosen to give Rei her homework. ' _Wait, where exactly is it that Rei lives?'_

The sound of the bell ringing caught everyone's attention as the class soon exited the room. Shinji pulled out the phone that Misato had given him. After waiting for a few minutes Misato picked up on the other end. "Hey, Shinji what is it?"

"Do, you know were Rei happens to live?" He put his homework within his school bag as he held on to her homework. Come to think of it he was wondering a lot about the girl lately. He had seen her not long after he got to Tokyo-3. In a vision of all things before he actually met her in person. It was mysterious and just before he had got into the Eva he had thought he heard her voice again in his mind. "I have her homework and I have no idea where I'm supposed to go to give it to her."

"I don't know myself though I'll look it up for yeah," Misato answered as Shinji waited for her response. After finally getting the address he set out for the train station.

* * *

Misato wanted to make sure she was hearing this right. Ritsuko had called her to talk about the prospect of her taking in another tenant. Well, actually she wanted to see if she wanted to take in two of them. The first one was the transfer pilot from the German branch, who after a lot of pressure from Gendo after finding out they wanted to come to Tokyo-3, was going to be staying here. The second one was the more surprising of the two. "You want Rei to move in with me and Shinji why?"

Ritsuko pulled out a picture of a run down and half collapsed building before her. "Because this is the state she lives in and I can't let her stay in such horrible conditions," Ritsuko would have brought her two her place if she could. The problem was as she found out that she couldn't when Gendo made her sign on as Rei watcher and caretaker while at NERV. Something told her he actually expected this. "I can't due to my contract and no one else wants to due to having to have Section 2 agents posted with them."

"And wouldn't that include me?" Misato would rather not have those men watching her. A few of them creeped her out.

Ritsuko shook her head at this. She had asked the commander about that tidbit after noticing their unsettling gazes to her. It was the only way he would sign off on her transfer. "As a trained member of the army, there wouldn't have any need to do so."

Well, that was one good point. Though Misato did question letting a young boy and a girl who were teenagers stay in the same building together. Especially given how off and emotionally broken Rei seemed to be. "What about the other pilot who are they?"

Ritsuko gave her the file. Opening it Misato was greeted with a picture of Asuka and made note that her eyes seemed to have misshapen pupils. The first thought that crossed her mind was having to house another girl. The second was the strangeness of the three pilots. She blinked at her deity report. "Wait, she's only been eating raw meat for years isn't that unhealthy?"

Ritsuko shrugged her shoulders at this. She tried to get an explanation on this but they didn't have much of an idea as to why. They suspected side effects of Eva piloting but exactly how was never looked into. "Apparently she has a trouble eating cooked meat and for some strange reason doesn't get sick when eating meat raw," Misato continued reading as the only other thing they commented on in her report caught her attention. "Along with a few other mutations."

"She has sharpened teeth?" Misato looked at Ritsuko to make sure that this wasn't a prank. Ritsuko just gave her a serious look. "You're serious."

"I had a similar reaction when I found out." Ritsuko was certain something was off to cause this sort of change. The moment she could she was going to look into getting a blood sample to test it and perhaps even one of Shinji's to compare it too. There was just something off.

Mistake closed the file as she thought this over. She had an extra room that she mostly just stuffed with some junk but could be fixed up. Still, sticking two girls to share it could be a hassle. ' _Or maybe not given how passive Rei is.'_ A sigh escaped Misato's lips. "I guess I'm going to have to clean up that extra room for the both of them."

Ritsuko had a smile at this. She knew she could trust Misato to help her. "Thank you."

* * *

The part of the city that Shinji was walking through was mostly torn down. Demolitions equipment lined the area along with the rumble from several of the buildings that had partly collapsed. ' _Does Rei's family live here?'_

He pulled up the paper with the address given to him just to make sure he was correct. The building where Rei lived was half fallen in. This was supposed to be owned by NERV and yet it looked like it was barely livable. Shinji took note of the Section 2 agents standing watch outside the building. They were practically the only people here. They seemed to just barely acknowledge him as he walked into the building.

Silence was all he could hear. There was no sounds or signs that anyone had lived here. It was like a ghost town. "Second-floor room five."

That was the apartment that Rei had. He was actually feeling very bad for her. Having to live here wondering if she even had things like running water. Pushing away his concerns he stood in front of the door to her apartment. Not a sound could be heard. "Rei are you there?"

He knocked a bit before noticing that the door was open slightly. He pulled the door open noticing that the lock was broken. Who lived like this in such a place? "I have your homework from school…" His eyes went wide as he watched Rei walk out of the bathroom without anything on and only handing the towel in her arms. It took him half a moment to realize that he was staring at her. "I-I-I s-sorry I-I should have w-waited."

Rei looked at him with confusion. She didn't know why he was acting like this. Rei having to undress for each of her LCL sessions hadn't quite grasped the concept of modesty. As far as she knew there was nothing wrong. "Why are you sorry?"

Shinji wondered if she was joking. After a few moments, it turned out that she wasn't. "I-I walked in on you while you were naked."

"Is that a problem?" Hearing this caused him to go wide-eyed in surprise. She really didn't have any clue about what he had just done. "Should I get dressed?"

' _How is that even a question?'_  The question on how Rei had such a disregard for modesty aside he would rather not listen to the small voice in his head telling him to take a look.

Shinji looked at the rundown apartment wondering why Rei was forced to live here. The buildings around it were all torn down. This one looked like it was half fallen apart as is. "I'm clothed now," Shinji turned back to see Rei in a simple pale blue dress. "I see you were chosen to bring my homework to me?"

He gave her a nod as he tried to fight back the image of Rei's naked form out of his head. A task that he was failing at completely. Embarrassed he tried to look away as he handed them to her. "Y-y-yeah, h-here."

Rei took the papers in her hand as she looked at them. Curious as to his behavior she reached out with her A.T. field to figure out what was wrong. ' _He thinks I'm pretty?'_  She felt her heartbeat race for just a moment at this. It confused her though she won't mind if she heard it again. "Thank you."

Shinji decided to left the apartment now that his mission was done. At least until Rei grabbed his arm and with surprising strength pulled him to her. "W-what?" He was suddenly facing her with his dual colored eyes looking straight into her red ones. ' _They are like rubies.'_

"Shinji what do you know about why we are fighting the Angels?" Rei's voice pulled him out of the minor trance that he was in.

Taking a moment he realized what she had asked him. He knew as much as the document that Misato gave him. "T-they caused Second Impact and if we don't stop them Then they'll kill everyone else."

Rei shook her head at this. Then again Gendo was likely to not tell anyone about everything he knew. Nor did he knew all it himself. "That's only partly true, Second Impact was caused by the Angel Adam but the war isn't as you are told."

Inwardly Shinji wanted to laugh at this. Of course, his father wasn't telling him everything. At this point, he wouldn't be surprised if he had remarried. "What is the truth then."

Rei sat on her bed and motioned for Shinji to join her. He hesitated for a moment before sitting on the rather plain and somewhat broken mattress. "There are actually two lines of Angels the one that we are fighting is the spawn of Adam, who are seeking their progenitor in order to preterm there own Third Impact as a means to terraform the planet for themselves."

That sort of cleared some things up. All the document said that the Angels were planning to wipe out humanity to conquer the world. Finding out that their goal was to locate their creator and terraform the world explained their motive. "Wait, you said there are two lines of Angels what is the other one?"

"Ours," Rei simply stated drawing confusion to Shinji. The blue haired girl continued on while his mind was racing, "Lilith is Adam's counterpart and she's been here just as long as he had it was her blood that mixed with the primordial oceans and created all life on the earth," She closed her eyes as she knew that the next part was going to be a lot to take in for him. "When she awoke Second Impact had already passed and in hopes of preventing Third Impact she created her own Angels though a fusion of both Angelic and Human in both body and soul," She turned to him looking him right into his eyes. "We are the Nephilim of Lilith."

Shinji looked at her not knowing what to say. It sounded outlandish. He wasn't some kind of half Angel monster! ' _Why do I sound so unsure though?'_  The image of the thing from his dreams returned again as he tried to push it away at this. "Y-y-you're joking right?"

Two looked at him before deciding that it was best to show him. To Shinji's shock two white wings shootout. They were long and gave off the appearance of being connected to her body like they were apart of her skin and back yet they were still just wings of light. A trait all angels had regardless of their lines. Shinji looked at her before the image of the thing from his dreams filled his vision before he fainted.

Shinji awoke as his eyes blurred in a haze. When his sight finally clear he was meet with Rei looking over him while he was in her bed. At first, he felt himself panic wondering what had happened before the memories hit him of what happened. Rei had told him everything and now he couldn't deny it. That thing he saw in his dreams was him. "H-how long was I out?"

"Only a few minutes," Rei could sense that he was starting to accept the truth. The hold on he had placed A.T. field was starting to weaken. Though it was still dormant at least it wouldn't be suppressed by him when he awoke his angelic nature.

So many questions ran through Shinji's mind. Why was he chosen to be one of these Nephilim? Furthermore wasn't he born human? "H-how did we end up like this?"

Rei looked on at him as Shinji started to realize the position they were in. A slight blush formed on his face at this. "I only know that both you and the Second Child were given it while you were still young allowing you both to develop into it as you age," That might explain why he couldn't remember it given how much of it he had forgotten. "I on the other have was made the way I was made from Lilith's own flesh and my soul birth from her own."

He didn't know much about Angels beyond what he had been told so far by both Misato's report and Rei. Even so, the way she was talking about Lilith made it sound like she was her mother. Still, She was awfully close to him and try as he might he couldn't push out his thoughts. "So, are you like her daughter?"

"She calls me as such and has been the only parent I have ever known," Talking about parents she knew Two should tell him about his. Especially just how cruel his mother really was.

A terrifying thought crossed his mind though. Did his father know that he was Nephilim? Rei looking at his expression noticed the panic and the slight increase in his breath as the horror of this crossed his mind. She made contact with her A.T. field to know what was on his mind. "Your father has no idea what either of us are as far as he knows you are still human."

Shinji's eyes widened at this. He was relieved to know that his dad wasn't using him for some kind of science experiment or a weapon. He literally wouldn't put it passed him. "Wait, how did you know what I was thinking?" He paused before realizing it had to be something that she could do thanks to her Angel powers. "You can read my mind?"

"In a since, I learned how to pick it up by reading your A.T. field it's something mother first taught me," Rei explained as she pulled back her field from him. "Like each Angel, our A.T. field has different properties and each of us have different abilities though like my mother I share the ability to read people via their A.T. field and contact them."

Suddenly he was starting to remember the position they were in. The talk about being able to read him made him go bright red. ' _Why do I smell blueberries?'_  His eyes widened as he realized he was smelling Rei's scent. To his surprise, Rei moved ever so closer to his face. ' _It can't be…'_

His mind went blank as Rei kissed him. The beating of his heart started to increase while unknown to him Rei felt her own heart increasing as well. She had no idea what came over her but a small pull told her to kiss him. For a second nothing happened before he kissed her back and for a brief second the two of them were actually kissing the other. When Rei pulled back the two looked at one another's eyes without saying a word.

Silence gripped the two of them as they simply looked unsure of what to say or even do. Finally, after seemingly a full minute Shinji finally spoke up. "I-I-I got to get b-back b-before Misato c-comes looking for me."

Rei gave him a nod as she moved off the bed and watched him leave. For a few moments, Rei continued to look on before putting her hands on her heart. ' _What is this feeling?'_ She closed her eyes as she recalled the feeling of the kiss. Her wings reappeared as her A.T. field fear out for a brief moment. As soon as it came it was gone. ' _Maybe I should ask my mother?'_

* * *

The Evangelion Unit-1 looked too anyone like it was just a big machine. The few that knew the truth about what they were made with an organic base would still have to agree that in function they fit the part. However, the darkest and most well-kept secret was that each Eva Unit held a soul of someone. This was why so few of them even existed. Each one of them was a prison. All except for Eva-1.

A lot more love and care went into its creation. For while the others were just made with a war in mind against the Angels this one serves another purpose in mind. Strictly speaking, it was far more developed and complex organically almost being a full grew angel outside of a few missing parts. After all, its soul didn't want to be trapped within a walking prison.

' _Something is wrong,'_  Yui awoke from her sleep having dreamed silently within her new body. The actions of using the Eva unit had slowly awoken her from this sleep. Everything was going as she had hoped. That is until she finally realized one thing was wrong. ' _My son isn't as I need him to be.'_

Yui felt something off with him. She didn't like unknown variables and she had planned for a host of them. If anyone was looking they would have noticed Eva-1's fingers twitch in annoyance. An action that Yui took note of. ' _What in the world.'_ It took her a few moments to locate why this was. If she could Yui would grin in joy at the surprising development. ' _An S2 organ!'_

There was one thing Yui couldn't seem to replicate when they were making the Eva's from the genetic remains of Adam or Lilith. The S2 organ was both biological and at the same time seemed almost magical in its nature. In theory, each of the Eva's could develop one. Though due to designs only Eva-1 was able to make any use of it as Yui was able to supervise it's making herself. ' _It's still developing but it would soon be functional and with it the first step of my plan.'_

How this came to be Yui didn't know but she wasn't going to deny such a gift. With the way things will go she suspected that she would soon have the others find her the remaining two keys for her plans and with them she could finally complete her vision.

* * *

Shinji walked into the apartment. His mind was still consumed on the realization that Rei had given him. He wasn't human like he had thought he was. It explained a lot about how he was. Why he had randomly developed his weird physical traits and his strength. Shinji looked at himself as he flexed his hand. ' _What does this even make me am I still who I am?'_

It seemed like an easy answer. However, the problem set in when he remembered that he had no idea what he was his whole life. He lived it thinking he was human when he actually wasn't. In a way, it seemed he was almost living a lie. "Oh, Shinji your back I had almost thought that you had gotten lost," His caretaker voice pulled him out of his thoughts as he watched her moving out some boxes from her extra room. "Now, I need your help getting the net room set up as a bedroom."

"Someone is moving in with us?" This was a surprise. Barely a week in Tokyo-3 and already things were changing around rather quickly. "Who is it?"

"Oh, Rei and the pilot transfer from Germany." Misato response caused Shinji to blink in surprise. He had just finished talking to Rei not too long ago and already they were going to be living together.

He was happy that she was moving out of that terrible building and he could get some answers on the whole Nephilim business. His mind, however, couldn't help but picture the kiss they had shared. The feeling on her lips on his and her scent on his nose still lingered. The thought of her living with them made him feel happy. "Wait, a pilot transfer from Germany?"

Misato gave him a nod before pulling out the picture she was given. "Her name is Asuka Langley Soryu, she's the second child and pilot of Eva-2." The thing that caught his attention was the oval-shaped pupils. He remembered Rei talking about how the Second Child was like the both of them. "Oh, and the raw meat with a yellow marker steak on it shouldn't be cook she can't actually eat cooked meat."

Eating uncooked meat sound rather unhealthy. Then again if she was a Nephilim then perhaps that wasn't a problem. "So, when will she get here?"

"I think we'll be meeting her tomorrow," Misato then remembered something. "Oh, right Ritsuko wanted you to prefer a harmonic test tomorrow as well with Rei and Asuka."

* * *

Asuka looked out the night sky as she stretched herself. Sitting for nearly two hours as the plane flew from Berlin to Tokyo-2. Eva-2 was being shipped out with the U.N. Aircraft carrier Over-The-Rainbow. Apparently, she was going to be transferred over to the main branch of NERV in Japan. ' _At least I am going to see some action hopefully.'_

She couldn't wait to see the two pilots that they had. Who knows maybe she'll see if the newbie actually had some skill outside of beginners luck.

**Notes for the Chapter:**

> Asuka has finally made it. The Nephilim of Lilith are nearly together. I can't wait to begin to write the interactions between the three of them. Now I think I have to explain something to S-01. Genetically speaking, Shinji and Rei genetic structures are altered by the angelic DNA. To some up they are not related to each other, in fact genetically speaking Shinji isn't Gendo and Yui child anymore. Explanations aside if you have a suggestion I won't mind looking into it and taking it into consideration.

**Author's Note:**

> So, to keep track we have SEELE, Yui, Gendo, and Lilith all having their own plans for the war with the Angels. Each one of them having goals that run counter to each other. Oh, and I picked a more unfavorable interruption of Yui motives because I figured if she is the daughter of someone in SEELE then she should be more like them in the thought process. That and because it's rather common practice (from what I have seen) for her to be heroic.
> 
> As for what Lilith's actions did to the first three children. Well, first off the effects of the DNA injects warps each of their genes (both human and angel) so there no genetic similarities. In case you were thinking about it.
> 
> I will be seeing all next chapter.


End file.
